An internal federal probe has concluded that Maurice Jones, Virginia Gov. Terry McAuliffe’s new commerce secretary, improperly lobbied Congress while he was in the Obama administration last year.

Mr. Jones, who was a deputy secretary at the U.S. Department of Housing and Urban Development, sent an email to more than 1,000 recipients — including 46 people at HUD — asking them to contact senators to “defend against efforts by some Republicans” to prevent a housing bill to come up for a vote, according to the internal probe. The message also asked “friends and supporters” to tell senators to vote “no” on another amendment.

A monthslong investigation by the HUD’s office of inspector general concluded that Mr. Jones and four others at HUD appear to have violated anti-lobbying laws, which restrict the use of funds for publicity or propaganda directed at pending legislation before Congress. The probe also concluded that Mr. Jones violated internal HUD policy on lobbying by federal employees.

Mr. Jones told investigators that he didn’t know about HUD’s policy prohibiting lobbying on pending legislation, according to a draft of the inspector general’s report expected to be released this week.

“[Deputy secretary] stated that it was articulated to him that ‘I could do things that others could not,’” investigators wrote in the report obtained by The Washington Times.

The Justice Department declined to open a criminal investigation into Mr. Jones, but the inspector general report said officials have referred their findings to the office of special counsel, which enforces federal laws that prohibit an official from coercing employees’ political activities. The Government Accountability Office also is conducting a review.

Phone and email messages to Mr. Jones and the Virginia Department of Commerce and Trade were not returned Monday.

A spokesman for HUD said officials are reviewing the inspector general’s findings.

“We take the issues raised in the report very seriously,” HUD spokesman Jereon Brown said. “We will continue to cooperate with ongoing investigations and will have no further comment while this matter and the report remains under review and cannot comment on personnel matters.”

The probe began after a request from Rep. Patrick T. McHenry, North Carolina Republican and chairman of the investigative subcommittee of the House Committee on Financial Services. He said the “directness and the specificity” of the email from Mr. Jones appeared to violate federal restrictions on lobbying by federal agencies.

Mr. McHenry’s panel will hold a hearing on the internal investigation Wednesday. In a letter last year to Mr. McHenry, HUD Secretary Shaun L.S. Donovan said the department had reviewed its guidance and ethics training.

The inspector general’s report singled out several other HUD employees, including Elliot Mincberg, acting general deputy assistant secretary. The inspector general found that he tried to interfere with the internal investigation by “interrupting and inserting himself into an ongoing witness interview.” He also threatened agents that he would ensure they were charged as a result of “inappropriate actions,” which he did not identify to investigators, the report said.

Mr. Mincberg told investigators that HUD had to protect the list of email recipients who received Mr. Jones‘ message, according to the report. Mr. Mincberg said his office had coordinated with “White House counsel,” and he asked the inspector general's office for assurances that the information wouldn’t be turned over to congressional Republicans, the report says.

Mr. Mincberg was not immediately available for comment late Monday.

Mr. Jones was named to Mr. McAuliffe’s Cabinet in January, and his biography on the state’s Commerce and Trade Department Web page makes prominent mention of his work at HUD.

He left well after the HUD inspector general had begun its review, but no mention of the probe was made when he departed.

Mr. Donovan called Mr. Jones a “tireless advocate” for HUD’s 8,000 employees in a statement after Mr. Jones accepted a job in Mr. McAuliffe’s Cabinet.

“Governor-Elect McAuliffe’s nomination today means that Maurice gets to go home to his family and his home state, where his public service career began,” Mr. Donovan said.

In 2012, The Washington Times reported that a federal financial disclosure form showed Mr. Jones pocketed more than a quarter-million dollars in bonus compensation as publisher of the Virginian-Pilot about the same time he was slashing newsroom jobs.